As part of a Facebook conversation Siddiqui, 45, defended the right of an individual to be called a martyr if he took up arms against Assad, and questioned whether those who fought against the Syrian president should face arrest upon return to the UK.

Former senior intelligence officials consider jihadists battling Assad's government forces in Syria to be a potential threat. They estimate that up to 300 fighters have already returned to the UK from Syria. Scotland Yard has warned that Britain will live with the terror legacy of the Syrian conflict for years to come.

The foreign secretary, William Hague, believes as many as 400 British citizens may be fighting in Syria, recently confirming that security measures are in place such as the option of withdrawing leave to remain, cancelling passports and arresting UK jihadists who have been fighting in Syria or for terrorist group Islamic State in Iraq and the Levant (Isis), which has seized control of swaths of northern Iraq.

Siddiqui, who ran Prevent in the south-west until 2012, pointed out that Britons were free to join the Israeli Defence Force and return to the UK without censure, while those taking up arms against what they viewed as a tyrannical dictator, Assad, faced arrest. He says he knew "nothing about" Isis at the time of the online conversation in February. He does not support the group.

Before generating headlines after sweeping into Iraq, Isis had been operating independently of other jihadist groups in Syria, including the al-Nusra Front, the official al-Qaida affiliate in the country, and has been involved in widespread infighting with other rebel groups.

Some Syrian rebels opposed to Isis point to instances of apparent hesitation by Assad's forces about attacking the group as evidence of tacit co-operation with the regime to undermine other rebel groups.

Writing on Facebook, in reference to the situation inside Syria, Siddiqui said: "If a man describes himself as wanting to help the oppressed and dies, in that case he is a martyr."

Referring to an individual prepared to travel and stand up for his beliefs, Siddiqui adds: "I'd rather take his word for it because he walked the walk and isn't sat behind a keyboard like me."

An Isis recruitment video showing three Britons – Reyaad Khan with school friend Nasser Muthana, from Cardiff, and a third man named as Abdul Raqib Amin, from Aberdeen – has fuelled anxieties over the radicalisation of Muslim youths in Britain as a result of the Syrian civil war.

Siddiqui told the Observer that he would be happy to endorse security measures on combatants if they applied to others returning from fighting abroad, not just Muslims. "As for people fighting in Syria, if they go with the intention to defend the civilian population from a dictator – a population we have abandoned – I accept their conviction until proven otherwise."